OpenRaiser/Intern-Atlas huggingface dataset:
Doc2OracLL: Investigating the Impact of Documentation on LLM-based Test Oracle Generation
Venue: arXiv cs.SE 2025
Year: 2025

Code documentation is a critical aspect of software development, serving as a bridge between human understanding and machine-readable code. Beyond assisting developers in understanding and maintaining code, documentation also plays a critical role in automating various software engineering tasks, such as test oracle generation (TOG). In Java, Javadoc comments provide structured, natural language documentation embedded directly in the source code, typically detailing functionality, usage, parameters, return values, and exceptions. While prior research has utilized Javadoc comments in test oracle generation (TOG), there has not been a thorough investigation into their impact when combined with other contextual information, nor into identifying the most relevant components for generating correct and strong test oracles, or understanding their role in detecting real bugs. In this study, we dive deep into investigating the impact of Javadoc comments on TOG.
From Intention To Implementation: Automating Biomedical Research via LLMs
Venue: arXiv cs.MA 2025
Year: 2025

Conventional biomedical research is increasingly labor-intensive due to the exponential growth of scientific literature and datasets. Artificial intelligence (AI), particularly Large Language Models (LLMs), has the potential to revolutionize this process by automating various steps. Still, significant challenges remain, including the need for multidisciplinary expertise, logicality of experimental design, and performance measurements. This paper introduces BioResearcher, the first end-to-end automated system designed to streamline the entire biomedical research process involving dry lab experiments. BioResearcher employs a modular multi-agent architecture, integrating specialized agents for search, literature processing, experimental design, and programming. By decomposing complex tasks into logically related sub-tasks and utilizing a hierarchical learning approach, BioResearcher effectively addresses the challenges of multidisciplinary requirements and logical complexity. Furthermore, BioResearcher incorporates an LLM-based reviewer for in-process quality control and introduces novel evaluation metrics to assess the quality and automation of experimental protocols. BioResearcher successfully achieves an average execution success rate of 63.07% across eight previously unmet research objectives. The generated protocols, on average, outperform typical agent systems by 22.0% on five quality metrics. The system demonstrates significant potential to reduce researchers' workloads and accelerate biomedical discoveries, paving the way for future innovations in automated research systems.
Efficient and Comprehensive Feature Extraction in Large Vision-Language Model for Pathology Analysis
Venue: arXiv cs.CV 2025
Year: 2025

Pathological diagnosis is vital for determining disease characteristics, guiding treatment, and assessing prognosis, relying heavily on detailed, multi-scale analysis of high-resolution whole slide images (WSI). However, existing large vision-language models (LVLMs) are limited by input resolution constraints, hindering their efficiency and accuracy in pathology image analysis. To overcome these issues, we propose two innovative strategies: the mixed task-guided feature enhancement, which directs feature extraction toward lesion-related details across scales, and the prompt-guided detail feature completion, which integrates coarse- and fine-grained features from WSI based on specific prompts without compromising inference speed. Leveraging a comprehensive dataset of 490K samples from diverse pathology tasks, we trained the pathology-specialized LVLM, OmniPath. Extensive experiments demonstrate that this model significantly outperforms existing methods in diagnostic accuracy and efficiency, providing an interactive, clinically aligned approach for auxiliary diagnosis in a wide range of pathology applications.
Obfuscated Activations Bypass LLM Latent-Space Defenses
Venue: arXiv cs.LG 2025
Year: 2025

Recent latent-space monitoring techniques have shown promise as defenses against LLM attacks. These defenses act as scanners that seek to detect harmful activations before they lead to undesirable actions. This prompts the question: Can models execute harmful behavior via inconspicuous latent states? Here, we study such obfuscated activations. We show that state-of-the-art latent-space defenses -- including sparse autoencoders, representation probing, and latent OOD detection -- are all vulnerable to obfuscated activations. For example, against probes trained to classify harmfulness, our attacks can often reduce recall from 100% to 0% while retaining a 90% jailbreaking rate. However, obfuscation has limits: we find that on a complex task (writing SQL code), obfuscation reduces model performance. Together, our results demonstrate that neural activations are highly malleable: we can reshape activation patterns in a variety of ways, often while preserving a network's behavior. This poses a fundamental challenge to latent-space defenses.
Infinite-dimensional next-generation reservoir computing
Venue: arXiv cs.LG 2025
Year: 2025

Next-generation reservoir computing (NG-RC) has attracted much attention due to its excellent performance in spatio-temporal forecasting of complex systems and its ease of implementation. This paper shows that NG-RC can be encoded as a kernel ridge regression that makes training efficient and feasible even when the space of chosen polynomial features is very large. Additionally, an extension to an infinite number of covariates is possible, which makes the methodology agnostic with respect to the lags into the past that are considered as explanatory factors, as well as with respect to the number of polynomial covariates, an important hyperparameter in traditional NG-RC. We show that this approach has solid theoretical backing and good behavior based on kernel universality properties previously established in the literature. Various numerical illustrations show that these generalizations of NG-RC outperform the traditional approach in several forecasting applications.
Connecting through Comics: Design and Evaluation of Cube, an Arts-Based Digital Platform for Trauma-Impacted Youth
Venue: arXiv cs.HC 2025
Year: 2025

This paper explores the design, development and evaluation of a digital platform that aims to assist young people who have experienced trauma in understanding and expressing their emotions and fostering social connections. Integrating principles from expressive arts and narrative-based therapies, we collaborate with lived experts to iteratively design a novel, user-centered digital tool for young people to create and share comics that represent their experiences. Specifically, we conduct a series of nine workshops with N=54 trauma-impacted youth and young adults to test and refine our tool, beginning with three workshops using low-fidelity prototypes, followed by six workshops with Cube, a web version of the tool. A qualitative analysis of workshop feedback and empathic relations analysis of artifacts provides valuable insights into the usability and potential impact of the tool, as well as the specific needs of young people who have experienced trauma. Our findings suggest that the integration of expressive and narrative therapy principles into Cube can offer a unique avenue for trauma-impacted young people to process their experiences, more easily communicate their emotions, and connect with supportive communities. We end by presenting implications for the design of social technologies that aim to support the emotional well-being and social integration of youth and young adults who have faced trauma.
Leveraging Multimodal Methods and Spontaneous Speech for Alzheimer's Disease Identification
Venue: arXiv cs.SD 2025
Year: 2025

Cognitive impairment detection through spontaneous speech is a promising avenue for early diagnosis of Alzheimer's disease (AD) and mild cognitive impairment (MCI), where timely intervention can significantly improve patient outcomes. The PROCESS Grand Challenge at ICASSP 2025 addresses these tasks by promoting innovative classification and regression methods for detecting cognitive decline. In this paper, we propose a multimodal fusion strategy that combines interpretable linguistic features with temporal embeddings extracted from pre-trained models. Our approach achieves an F1-score of 0.649 for the classification task (predicting healthy, MCI, dementia) and an RMSE of 2.628 for the regression task (MMSE score prediction), securing the top overall ranking in the competition.
Large Language Models for Persian $ \leftrightarrow $ English Idiom Translation
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) have shown superior capabilities in translating figurative language compared to neural machine translation (NMT) systems. However, the impact of different prompting methods and LLM-NMT combinations on idiom translation has yet to be thoroughly investigated. This paper introduces two parallel datasets of sentences containing idiomatic expressions for Persian$\rightarrow$English and English$\rightarrow$Persian translations, with Persian idioms sampled from our PersianIdioms resource, a collection of 2,200 idioms and their meanings, with 700 including usage examples. Using these datasets, we evaluate various open- and closed-source LLMs, NMT models, and their combinations. Translation quality is assessed through idiom translation accuracy and fluency. We also find that automatic evaluation methods like LLM-as-a-judge, BLEU, and BERTScore are effective for comparing different aspects of model performance. Our experiments reveal that Claude-3.5-Sonnet delivers outstanding results in both translation directions. For English$\rightarrow$Persian, combining weaker LLMs with Google Translate improves results, while Persian$\rightarrow$English translations benefit from single prompts for simpler models and complex prompts for advanced ones.
A General Safety Framework for Autonomous Manipulation in Human Environments
Venue: arXiv cs.RO 2025
Year: 2025

Autonomous robots are projected to significantly augment the manual workforce, especially in repetitive and hazardous tasks. For a successful deployment of such robots in human environments, it is crucial to guarantee human safety. State-of-the-art approaches to ensure human safety are either too conservative to permit a natural human-robot collaboration or make strong assumptions that do not hold for autonomous robots, e.g., knowledge of a pre-defined trajectory. Therefore, we propose the shield for Safe Autonomous human-robot collaboration through Reachability Analysis (SARA shield). This novel power and force limiting framework provides formal safety guarantees for manipulation in human environments while realizing fast robot speeds. As unconstrained contacts allow for significantly higher contact forces than constrained contacts (also known as clamping), we use reachability analysis to classify potential contacts by their type in a formally correct way. For each contact type, we formally verify that the kinetic energy of the robot is below pain and injury thresholds for the respective human body part in contact. Our experiments show that SARA shield satisfies the contact safety constraints while significantly improving the robot performance in comparison to state-of-the-art approaches.
Ensuring Force Safety in Vision-Guided Robotic Manipulation via Implicit Tactile Calibration
Venue: arXiv cs.RO 2025
Year: 2025

In dynamic environments, robots often encounter constrained movement trajectories when manipulating objects with specific properties, such as doors. Therefore, applying the appropriate force is crucial to prevent damage to both the robots and the objects. However, current vision-guided robot state generation methods often falter in this regard, as they lack the integration of tactile perception. To tackle this issue, this paper introduces a novel state diffusion framework termed SafeDiff. It generates a prospective state sequence from the current robot state and visual context observation while incorporating real-time tactile feedback to refine the sequence. As far as we know, this is the first study specifically focused on ensuring force safety in robotic manipulation. It significantly enhances the rationality of state planning, and the safe action trajectory is derived from inverse dynamics based on this refined planning. In practice, unlike previous approaches that concatenate visual and tactile data to generate future robot state sequences, our method employs tactile data as a calibration signal to adjust the robot's state within the state space implicitly. Additionally, we've developed a large-scale simulation dataset called SafeDoorManip50k, offering extensive multimodal data to train and evaluate the proposed method. Extensive experiments show that our visual-tactile model substantially mitigates the risk of harmful forces in the door opening, across both simulated and real-world settings.
VibrantVS: A high-resolution multi-task transformer for forest canopy height estimation
Venue: arXiv cs.CV 2025
Year: 2025

This paper explores the application of a novel multi-task vision transformer (ViT) model for the estimation of canopy height models (CHMs) using 4-band National Agriculture Imagery Program (NAIP) imagery across the western United States. We compare the effectiveness of this model in terms of accuracy and precision aggregated across ecoregions and class heights versus three other benchmark peer-reviewed models. Key findings suggest that, while other benchmark models can provide high precision in localized areas, the VibrantVS model has substantial advantages across a broad reach of ecoregions in the western United States with higher accuracy, higher precision, the ability to generate updated inference at a cadence of three years or less, and high spatial resolution. The VibrantVS model provides significant value for ecological monitoring and land management decisions, including for wildfire mitigation.
Reinforcement Learning Enhanced LLMs: A Survey
Venue: arXiv cs.CL 2025
Year: 2025

Reinforcement learning (RL) enhanced large language models (LLMs), particularly exemplified by DeepSeek-R1, have exhibited outstanding performance. Despite the effectiveness in improving LLM capabilities, its implementation remains highly complex, requiring complex algorithms, reward modeling strategies, and optimization techniques. This complexity poses challenges for researchers and practitioners in developing a systematic understanding of RL-enhanced LLMs. Moreover, the absence of a comprehensive survey summarizing existing research on RL-enhanced LLMs has limited progress in this domain, hindering further advancements. In this work, we are going to make a systematic review of the most up-to-date state of knowledge on RL-enhanced LLMs, attempting to consolidate and analyze the rapidly growing research in this field, helping researchers understand the current challenges and advancements. Specifically, we (1) detail the basics of RL; (2) introduce popular RL-enhanced LLMs; (3) review researches on two widely-used reward model-based RL techniques: Reinforcement Learning from Human Feedback (RLHF) and Reinforcement Learning from AI Feedback (RLAIF); and (4) explore Direct Preference Optimization (DPO), a set of methods that bypass the reward model to directly use human preference data for aligning LLM outputs with human expectations. We will also point out current challenges and deficiencies of existing methods and suggest some avenues for further improvements. Project page of this work can be found at https://github.com/ShuheWang1998/Reinforcement-Learning-Enhanced-LLMs-A-Survey.
SVGFusion: Scalable Text-to-SVG Generation via Vector Space Diffusion
Venue: arXiv cs.CV 2025
Year: 2025

In this work, we introduce SVGFusion, a Text-to-SVG model capable of scaling to real-world SVG data without relying on text-based discrete language models or prolonged Score Distillation Sampling (SDS) optimization. The core idea of SVGFusion is to utilize a popular Text-to-Image framework to learn a continuous latent space for vector graphics. Specifically, SVGFusion comprises two key modules: a Vector-Pixel Fusion Variational Autoencoder (VP-VAE) and a Vector Space Diffusion Transformer (VS-DiT). The VP-VAE processes both SVG codes and their corresponding rasterizations to learn a continuous latent space, while the VS-DiT generates latent codes within this space based on the input text prompt. Building on the VP-VAE, we propose a novel rendering sequence modeling strategy which enables the learned latent space to capture the inherent creation logic of SVGs. This allows the model to generate SVGs with higher visual quality and more logical construction, while systematically avoiding occlusion in complex graphic compositions. Additionally, the scalability of SVGFusion can be continuously enhanced by adding more VS-DiT blocks. To effectively train and evaluate SVGFusion, we construct SVGX-Dataset, a large-scale, high-quality SVG dataset that addresses the scarcity of high-quality vector data. Extensive experiments demonstrate the superiority of SVGFusion over existing SVG generation methods, establishing a new framework for SVG content creation. Code, model, and data will be released at: https://ximinng.github.io/SVGFusionProject/
Grid: Omni Visual Generation
Venue: arXiv cs.CV 2025
Year: 2025

Visual generation has witnessed remarkable progress in single-image tasks, yet extending these capabilities to temporal sequences remains challenging. Current approaches either build specialized video models from scratch with enormous computational costs or add separate motion modules to image generators, both requiring learning temporal dynamics anew. We observe that modern image generation models possess underutilized potential in handling structured layouts with implicit temporal understanding. Building on this insight, we introduce GRID, which reformulates temporal sequences as grid layouts, enabling holistic processing of visual sequences while leveraging existing model capabilities. Through a parallel flow-matching training strategy with coarse-to-fine scheduling, our approach achieves up to 67 faster inference speeds while using <1/1000 of the computational resources compared to specialized models. Extensive experiments demonstrate that GRID not only excels in temporal tasks from Text-to-Video to 3D Editing but also preserves strong performance in image generation, establishing itself as an efficient and versatile omni-solution for visual generation.
ThreatPilot: Attack-Driven Threat Intelligence Extraction
Venue: arXiv cs.CR 2025
Year: 2025

Efficient defense against dynamically evolving advanced persistent threats (APT) requires the structured threat intelligence feeds, such as techniques used. However, existing threat-intelligence extraction techniques predominantly focuses on individual pieces of intelligence-such as isolated techniques or atomic indicators-resulting in fragmented and incomplete representations of real-world attacks. This granularity inherently limits on both the depth and the contextual richness of the extracted intelligence, making it difficult for downstream security systems to reason about multi-step behaviors or to generate actionable detections. To address this gap, we propose to extract the layered Attack-driven Threat Intelligence (ATIs), a comprehensive representation that captures the full spectrum of adversarial behavior. We propose ThreatPilot, which can accurately identify the AITs including complete tactics, techniques, multi-step procedures, and their procedure variants, and integrate the threat intelligence to software security application scenarios: the detection rules (i.e., Sigma) and attack command can be generated automatically to a more accuracy level. Experimental results on 1,769 newly crawly reports and 16 manually calibrated reports show ThreatPilot's effectiveness in identifying accuracy techniques, outperforming state-of-the-art approaches of AttacKG by 1.34X in F1 score. Further studies upon 64,185 application logs via Honeypot show that our Sigma rule generator significantly outperforms several existing rules-set in detecting the real-world malicious events. Industry partners confirm that our Sigma rule generator can significantly help save time and costs of the rule generation process. In addition, our generated commands achieve an execution rate of 99.3%, compared to 50.3% without the extracted intelligence.
Adaptive Reward Design for Reinforcement Learning
Venue: arXiv cs.RO 2025
Year: 2025

There is a surge of interest in using formal languages such as Linear Temporal Logic (LTL) to precisely and succinctly specify complex tasks and derive reward functions for Reinforcement Learning (RL). However, existing methods often assign sparse rewards (e.g., giving a reward of 1 only if a task is completed and 0 otherwise). By providing feedback solely upon task completion, these methods fail to encourage successful subtask completion. This is particularly problematic in environments with inherent uncertainty, where task completion may be unreliable despite progress on intermediate goals. To address this limitation, we propose a suite of reward functions that incentivize an RL agent to complete a task specified by an LTL formula as much as possible, and develop an adaptive reward shaping approach that dynamically updates reward functions during the learning process. Experimental results on a range of benchmark RL environments demonstrate that the proposed approach generally outperforms baselines, achieving earlier convergence to a better policy with higher expected return and task completion rate.
DCSEG: Decoupled 3D Open-Set Segmentation using Gaussian Splatting
Venue: arXiv cs.CV 2025
Year: 2025

Open-set 3D segmentation represents a major point of interest for multiple downstream robotics and augmented/virtual reality applications. We present a decoupled 3D segmentation pipeline to ensure modularity and adaptability to novel 3D representations as well as semantic segmentation foundation models. We first reconstruct a scene with 3D Gaussians and learn class-agnostic features through contrastive supervision from a 2D instance proposal network. These 3D features are then clustered to form coarse object- or part-level masks. Finally, we match each 3D cluster to class-aware masks predicted by a 2D open-vocabulary segmentation model, assigning semantic labels without retraining the 3D representation. Our decoupled design (1) provides a plug-and-play interface for swapping different 2D or 3D modules, (2) ensures multi-object instance segmentation at no extra cost, and (3) leverages rich 3D geometry for robust scene understanding. We evaluate on synthetic and real-world indoor datasets, demonstrating improved performance over comparable NeRF-based pipelines on mIoU and mAcc, particularly for challenging or long-tail classes. We also show how varying the 2D backbone affects the final segmentation, highlighting the modularity of our framework. These results confirm that decoupling 3D mask proposal and semantic classification can deliver flexible, efficient, and open-vocabulary 3D segmentation.